"Working with the Marlins this past season has been one of the most rewarding experiences of my baseball career," he wrote. "I am grateful and humbled that Jeffrey Loria and the Marlins gave me the opportunity to be a part of their organization. Though my contract was only for one year, I enjoyed sharing my hitting knowledge and other aspects of the game with such a talented group of players.
"I am proud of the their development and accomplishments over the course of the season and hope they will be able to continue to build off their hard work as they head into next year. I look forward to what the future holds for me - but I do know that baseball is and always will be in my blood."
Bonds made a full-time return to baseball this season when he joined the Marlins. Owner Jeffrey Loria first suggested hiring the steroids-tainted home run king and new manager Don Mattingly went along with the idea.
But the Marlins improved only marginally under the slugging great.
The Marlins this season scored 655 runs, which ranked ahead of only the Braves and Phillies in the National League.
Mattingly said the organization decided to move in a different direction with its coaching staff.
"I don't need to get into the reasons really with anything with Barry," Mattingly said. "We feel like any time you talk about coaches and letting someone go those are not easy things to talk about. We'll just try to get the best guy for the situation."
Bonds, who hit 762 home runs, ended his playing career in 2007.
The Marlins also fired third base coach Lenny Harrisand bullpen coach Reid Cornelius as part of the changes on Wednesday.